Wilkinson was involved in an altercation with the City striker which was not seen by the match officials but was caught on video.
Balotelli went down after an apparent off-the-ball clash with Wilkinson, the pair having shadowed each other most of the afternoon.
Referee Mark Clattenburg spoke to the players but took no action and replays did not suggest anything serious had occurred.
Wilkinson now has until 6pm on Wednesday 19 September 2012 to respond to the charge.
Source: PA
Source: PA